Ontology
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From Document Silos to Process Intelligence: A Multi-Layer Knowledge Graph for CMC Process Development
2026-09-10 12:59:04Reza Amirmoshiri, Faryad Sahneh, Yasser JangjouAbstract
Chemistry, Manufacturing and Controls (CMC) process development generates an enormous body of technical information across a multi-stage, knowledge-intensive continuum from drug discovery to commercial manufacturing. This knowledge is traditionally fragmented across functions and heterogeneous formats, causing traceability gaps and significant knowledge-management costs during technology transfer and regulatory filing. We present a modular agentic-AI platform that converts a heterogeneous corpus of process-development documents into a queryable, dual-layer knowledge graph. A base knowledge layer builds a lexical graph with a Document-Section-Chunk hierarchy through lossless ingestion of digital, scanned, handwritten, and multilingual documents, while an intelligence layer extracts ontology-aligned entities and bridges cross-document concepts through a provenance-anchored domain graph. LLM agents operate across both layers, selecting the retrieval path best suited to each question. We evaluate the lexical layer with a novel three-tier protocol measuring the deployment-fidelity of a retrieval-augmented generation (RAG) system on proprietary data, demonstrated on 505 questions curated from 38 development reports of a Sanofi small-molecule program. Tier-1 multiple-choice accuracy of 95% signals strong platform reliability; the stricter Tier-2 LLM-judge pass rate of 85%, which degrades on comparative and corpus-wide questions, reveals a failure taxonomy that Tier-1 accuracy alone fails to capture. A router agent selects between layers according to question type. We anticipate this protocol will enable future designers of agentic platforms to assess their systems against nonpublic databases, and that graph-based architectures will see broader adoption in pharma as a means of transforming fragmented document repositories into structured process intelligence.
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https://arxiv.org/abs/2609.11493
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Fortunate Recall: Ontology-Driven Memory Lifecycle Management for Persistent Coherence in LLMs
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Current LLM memory systems treat all personal facts identically, so stores grow without bound while retrieval precision degrades. The core challenge is lifecycle management: which memories should persist, which should be replaced, and at what rate, conditioned on the behavioral type of each fact. Fortunate Recall (FR) is a composable policy layer that classifies personal facts into a 10+1 behavioral ontology and applies category-specific lifecycle policies (differential temporal decay, slot-key supersession, event-time validity, and category-aware retrieval routing) as deterministic functions over LLM-extracted metadata. FR-Bank, our infrastructure-independent implementation, reaches a 76.9% pass rate on LifecycleBench, a new 516-question temporal-disambiguation benchmark, ahead of Mem0, A-MEM, Memory-R1, and MemoryOS (61% to 70.5%), and 75.2% on the full LongMemEval-S under the canonical Wu et al. judge protocol, so lifecycle policies impose no measurable cost on standard retrieval. A pre-registered ablation locates the gains: replacing the typed layer with three generic lifecycle primitives leaves correctness statistically unchanged (-1.7pp, 95% CI [-6.0, +2.7]), so the generic lifecycle metadata carries the correctness advantage, while the behavioral ontology carries calibration, halving downstream confabulation (12.0% vs 24.2%, p<0.001). End-to-end, FR-Bank cuts confabulation from Mem0's 45.1% to 22.4% over answered queries and from 32.2% to 13.0% over all queries while answering more of them correctly (31.2% vs 18.6%); the ranking replicates on the open-weight Kimi K2.5. The decomposition transfers to BEAM, an independently built benchmark: 46.8% correct vs Mem0's 32.9% over 280 questions, with the ontology's benefit concentrated in contradiction resolution and saturating near seven policy clusters. The ontology, benchmark, and code are released.
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https://arxiv.org/abs/2609.10413
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OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization
2026-09-09 11:30:25Jie Song, Zhichuan Xu, Ziyu Lu, Meng Xiao, Cheng Bi, Yuxin Zhang, Xin Zheng, Xiaoran Li, Qiongfang Cao, Hao Yang, Bairong ShenAbstract
Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at this https URL.
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https://arxiv.org/abs/2609.10055
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Can We Trust Video Hallucination Detectors? VidHalLoc for Evaluating the Evaluators
2026-09-09 08:52:23Xinyu Chen, Adnan Mahmood, Mark DrasAbstract
Video-language models and video agents can produce hallucinations that conflict with spatiotemporal evidence. Existing benchmarks mainly evaluate model hallucinations, and heterogeneous mechanisms make detector reliability difficult to compare. We introduce VidHalLoc, a benchmark that evaluates hallucination detection methods under a unified diagnostic evaluation protocol using 2,000 adversarial hallucination samples across Video Question Answering and Video Captioning tasks, spanning Ontology and Dynamic hallucination categories. To construct VidHalLoc efficiently, we introduce VideoHALO, a Harness Engineering-informed multi-agent workflow that decomposes data construction into four executable stages supported by a memory system and a communication protocol. Evaluation of fifteen methods reveals that the four dedicated detectors peak at an Overall accuracy of only 34.63%, indicating limited reliability across video hallucination types [Dataset Repository: this https URL].
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https://arxiv.org/abs/2609.09895
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OntoKG-EQ: A provenance-grounded, competency-question-governed knowledge graph for auditable analyst querying
2026-09-08 15:11:38Furqan Nasir, Muhammad Atif Saeed, Muhammad Ehsan, Sher Jeel Ahmad, Abdul Moiz AltafAbstract
Analysts in emerging equity markets keep answering the same questions. Did fundamentals match the market's response? How does the local currency co-move with returns? Which firms outperform sector and benchmark, and which disclosures coincide with abnormal trading? These answers come from ad-hoc spreadsheets that are hard to reproduce, audit, or trust. We present OntoKG-EQ, a knowledge-based system that makes such queries reproducible, evidence-linked, temporally explicit, valid, and inspectable. It couples a bounded, competency-question-governed core ontology with a provenance-aware knowledge graph in which every class, property, shape, and metric is justified by one of five frozen questions. The system materialises market data into the graph, computes the metrics, validates its structure against declarative shape constraints, answers each competency question with a graph query, derives typed findings, and generates an explanation tracing each result to its observations, evidence, sources, and provenance. We evaluate on curated datasets from three emerging markets (Pakistan, Malaysia, Indonesia). Once each market's data is mapped into the common schema, the ontology, shapes, queries, and rules are reused unchanged. A relational-database baseline shows the graph changes no analytics. Its value is governance, provenance, and self-explaining structure. Because answers are rendered deterministically from the validated graph, their consistency with it is guaranteed by construction. Used as a reference, the system measures how consistently eight open language models transcribe the same evidence (provenance coverage 0.00 to 1.00). A study with a 17-participant convenience panel finds the evidence bundle significantly increased perceived trust and completeness. Code and data are openly released.
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URL
https://arxiv.org/abs/2609.08869
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Evidence-Grounded Retrieval for Investigation Hunt Lead Generation from CTI Reports
2026-09-08 14:21:35Akash Prakash, Boubakr Nour, Makan Pourzandi, Chadi Assi, Mourad DebbabiAbstract
Threat hunting increasingly depends on converting unstructured knowledge (e.g., Cyber Threat Intelligence reports) into actionable hunt leads: concise, investigable hypotheses grounded in observable artifacts and adversary techniques. Producing such leads manually is a tedious and hard-to-scale task. Existing automated approaches stop at the entity layer, ignore the defender's operational environment, and analyze each report in isolation. To address these gaps, we introduce AHLERT, a system that automatically extracts relevant, environment-aware, and hunt leads from threat reports through (i) a hybrid retriever that combines dense vector search with multi-hop traversal over a knowledge graph seeded with MITRE ATT&CK; (ii) an ontology-grounding retrieval-augmented generation method that constrains each lead to the defender's own assets and controls; and (iii) an LLM-agnostic framework that emits structured, directly actionable leads rather than loose indicators of compromise. We evaluate AHLERT on public CTI reports for well-known APTs across multiple proprietary and open-weight models. Hybrid evidence retrieval with ontology grounding raises mean F1 by ~2x (0.44 to 0.85) over a single-route flat-RAG baseline, and AHLERT attains the highest effectiveness score (~86.95%) compared with off-the-shelf LLM models.
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https://arxiv.org/abs/2609.08790
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OntologyBench: Can Dense Retrieval Satisfy Structured Biomedical Constraints?
2026-09-08 03:04:36Xiao Yu Cindy Zhang, Wyeth Wasserman, Jian ZhuAbstract
We introduce OntologyBench, a tiered biomedical retrieval benchmark comprising 471,854 training and 125,744 evaluation query-document relevance pairs across concept grounding, relational retrieval, and compositional phenotype-based retrieval. Although these tasks can be tractable using ontology-aware reference methods, across task tiers, embedding performance is generally lower on relational and compositional tasks than on concept-grounding tasks. Fine-tuning on ontology-derived supervision improves performance on several relational and compositional tasks, whereas the evaluated reranking and LLM-based candidate-scoring methods provide little or no end-to-end improvement. Errors frequently reflect diseases matching only subsets of the phenotype evidence. These findings indicate that the evaluated embedding and reranking configurations do not reliably recover the compatibility encoded by the selected ontology relations and phenotype combinations and motivate retrieval systems that better integrate learned representations with structured biomedical knowledge.
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https://arxiv.org/abs/2609.08174
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Large Language Models for HVAC Operations in Building Energy Systems: A Critical Review of Methods, Applications, and Deployment Readiness
2026-09-04 16:08:05Alexander Neubauer, Tianzhen Hong, Han Li, Mengbo Yu, Amin Darbandi, Yannick F\"urst, Martin KriegelAbstract
Building automation systems generate rich sensor data yet remain insight-poor because heterogeneous point naming, missing metadata, and fragmented documentation obstruct their operational use. This systematic review analyses and codes 66 peer-reviewed studies on large language models (LLMs) for HVAC operations published between 2023 and March 2026. Each study is classified across five application families and three LLM method families and assessed for evidence realism, deployment readiness, and the responsibility boundary between the LLM and physical HVAC decisions. The corpus is concentrated in building energy modelling (BEM, 32 of 66 papers), while load forecasting remains too sparse for subfield-level conclusions. Only four studies reach pilot-level evidence, and none reports sustained operational deployment. No study was classified as ready-now for industry adoption; three were near-term and 63 research-only. Nevertheless, several bounded, human-in-the-loop uses merit near-term trials, including point-name normalisation, document-grounded operator support, BEM workflow assistance, and advisory interfaces around physics-based controllers. Conventional machine learning (ML), model predictive control (MPC), reinforcement learning (RL) and ontology-based tools remain more adopted for high-frequency control, short-horizon numerical forecasting, and well-posed ontology mapping, while autonomous agentic operation and unvalidated occupant proxies remain research-stage. Current evidence therefore supports LLMs primarily as semantic and workflow layers rather than autonomous HVAC controllers. Future work should prioritise field-validated benchmarks, orchestration evaluation under operational constraints, and LLM-MPC/RL architectures with bounded latency and verifiable safety properties.
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https://arxiv.org/abs/2609.05314
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NS-ST-GraphRAG: Neuro-Symbolic Spatio-Temporal GraphRAG for Literary Knowledge Processing
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Long-form literary narratives pose a distinctive information-processing challenge for retrieval-augmented generation: relevant evidence is distributed across chapters, relations evolve over narrative time, and correct answers may depend jointly on temporal, spatial, and relational constraints. We propose NS-ST-GraphRAG, a neuro-symbolic spatio-temporal GraphRAG framework that integrates ontology-guided extraction, deterministic constraint checking, dual temporal coordinates, spatial scene attributes, and dynamic sub-graph retrieval. Instead of retrieving from a single corpus-level graph, the framework selects the graph state valid for the temporal and spatial scope of a query and grounds generated answers in traceable evidence. We further introduce Red-Chamber-QA, to our knowledge the first open multi-hop question-answering benchmark for classical Chinese literature, with time-, space-, and general-question categories, per-part evidence spans, and deterministic shortcut controls. On a 120-question held-out split, NS-ST-GraphRAG achieves mechanical answer reproduction of 0.733 versus 0.675 for the frozen window baseline and 0.083 for a closed-book model (McNemar exact p = 0.092, directionally favorable but not significant); semantic-judge accuracy is 0.866 versus 0.850. The pre-specified constrained-category condition of H2 is not supported by the delivered comparison. These results show how temporal graph representation, constrained extraction, and auditable evaluation integrate into a unified framework for verifiable knowledge processing over long-form narrative.
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https://arxiv.org/abs/2609.05139
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Corporate Language Model : Transforming Tacit and Fragmented Enterprise Knowledge into a Sovereign, Auditable, and Executable Corporate Intelligence Layer
2026-09-03 18:39:07Fabricio C. Avini, Guilherme TrezAbstract
Enterprise AI deployments fail not from model inadequacy, but because organizations lack a structured substrate encoding how they decide, negotiate, and execute. Generic LLMs carry no firm-specific ontological priors; RAG remains brittle, with no path to executable action; static playbooks encode logic but cannot reason or adapt. This demands an architecture treating tacit-knowledge capture, ontological grounding, sovereign deployment, and auditable actuation as co-designed from the start. This paper introduces the Corporate Language Model (CLM), a framework transforming a firm's structured, unstructured, multimodal, and tacit knowledge into an ontology-grounded enterprise foundation upon which reasoning and governed execution are composed. CLM has five capability planes and four architectural pillars: a Neurosymbolic Mesh coupling generative models with a knowledge graph; a Skill Graph where reusable tactics, personas, objections, and goals are typed and composed; Living Digital Twins modeling functional areas as reasoning surrogates; and a Deep Security Layer enforcing sovereignty, traceability, and human oversight. A Spec-as-Code paradigm bridges grounded intent and executable artifact. CLM is one instantiation of this foundation-centric class. Four contributions follow: CLM is defined as a distinct object of study; the Skill Graph is introduced for compositional explainability by construction; the Wisdom Listener effect is proposed, whereby tacit-capable foundations compound in value with use, connecting to dynamic capabilities and organizational learning; and evidence from a JCI-accredited tertiary hospital in Brazil instantiates three of the six maturity stages under LGPD.
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https://arxiv.org/abs/2609.04377
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A hybrid pipeline for dynamic ontology-based semantic mapping
2026-09-03 14:11:21Konstantinos Dimitropoulos, Ioannis HatzilygeroudisAbstract
Semantic mapping plays a crucial role in the ability of a robot to interact with objects, operate and navigate a complex environment. The most common pipeline for semantic mapping consists of geometric mapping and localization (SLAM), perception, semantic fusion and semantic representation. However, more recent works also integrate a form of prior knowledge in their application, most notably knowledge graphs or semantic scene graphs, to improve contextual understanding of the environment. In this paper, we present a hybrid pipeline for semantic mapping. Our system incorporates an external calibrated camera using homography projection for geometric mapping and localization, combined with object detection, persistent object tracking and ontology driven semantic updates to build a dynamic semantic world model. Linear regression models are also used for correction of the estimated values of real world coordinates. The system continuously updates object instances, spatial properties and semantic relations based on real time sensory data. Ontologies are selected as form of knowledge representation due to their hierarchical structure, semantic expressiveness and support for dynamic world modelling.
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https://arxiv.org/abs/2609.03891
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Learning to Fuse LLMs with Ontology Rankers for Rare-Disease Diagnosis
2026-09-02 11:44:21Zhaoyang Jiang, Zhizhong Fu, Yunsoo Kim, Zicheng Li, Xuanqi Peng, Fei Teng, Jiacong Mi, Honghan WuAbstract
Ontology rankers remain useful for rare-disease diagnosis because each candidate can be traced to matched patient phenotypes. Large language models (LLMs) can generate differential diagnoses from the same patient description, but their predictions lack an equally clear evidence trail. Rather than asking which system should replace the other, we ask whether an LLM can improve the ranker without giving up its evidence. Our behavior-based fusion model examines the two ranked lists, their agreement, and the ontology support behind each candidate, and learns how much to rely on each system for the individual case. Before comparison, we remove a documented test-set leakage pathway caused by benchmark cases and ontology annotations being derived from the same publications. Across eight open LLMs, fusion improves Phenomizer Recall@1 by 7.86 percentage points on Phenopacket Store and 20.18 points on RAMEDIS. When paired with DeepSeek-V4-Flash through an API, a fusion model trained only on the other LLMs improves Recall@1 from 0.1657 to 0.2176, a 5.19-point gain, without retraining. For 90.8% of correct fused diagnoses, the disease retains candidate-level ontology evidence that can be inspected. These results show that LLMs can strengthen an established diagnostic tool without discarding the structured evidence that makes it useful.
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https://arxiv.org/abs/2609.02473
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Towards a Foundational Ontology for Identifying and Resolving Contradictions in Dialogue-based Human-Robot Interactions
2026-09-02 09:35:02Maitreyee Tewari, Michele PersianiAbstract
Existing Human-Robot Interaction (HRI) literature has focused on identifying and structuring errors, failures, conflicts, and knowledge issues (called in this work as contradictions) in domain-specific dialogue-based interactions. However, there is still lack of a formal computational framework to represent and define these contradictions, interoperable and usable across HRI and human-agent interaction (HAI) domains. Thus, this research project aims to capture, represent, and evaluate the notion of (1) dialogue-based collaborative interaction and (2) related contradictions in a foundational ontology. METHONTOLOGY, a systematic approach to build domain-independent ontologies was applied. In the conceptualisation stage of the presented ontology, concepts and models from Activity Theory were used. Preliminary results presented in this short article are: (i) Natural language definitions of dialogues and related contradictions in HRI, (ii) Set Theoretic definitions of dialogues and contradictions, and (iii) First Order Logic (FoL) formulation of the contradiction concepts and three novel principles guiding dialogue-based interactions between humans and robots. In summary, we report on ongoing work to develop a foundational ontology based on Activity Theory called Activity Theory-based foundational ontology (ATFOt) to capture and represent the notion of contradictions in HRI.
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https://arxiv.org/abs/2609.02364
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SCX Router: Streaming Zero-Shot Model Selection with a Decoder-KV Classifier and a Real-World Task Ontology
2026-09-02 08:40:07Ihor Stepanov, Aleksandr Smechov, Mykhailo Shtopko, Dmytro Vodianytskyi, Oleksandr LukashovAbstract
The rapid proliferation of large language models (LLMs) and the growing diversity of their applications presents a unique optimization opportunity: selecting the right model for the task, while optimizing for speed, cost, and quality at a per-task level. However, inference endpoints can vary widely in quality, price, latency, context support, tool use, domain expertise, and reasoning behavior. This heterogeneity makes manual heuristics difficult to maintain and unlikely to achieve consistently favorable speed--cost--quality trade-offs on their own. We introduce \router{}, a lightweight GLiClass-based router that assigns a suitability score to each inference-time model label without autoregressive generation. The released 0.6B-parameter checkpoint combines a Qwen3 decoder with a shallow bidirectional scorer. Its decoder-KV execution path preserves a text-only key--value cache across a session, encodes only new dialogue turns, and evaluates transient candidate-label tokens without adding them to the persistent cache. The same checkpoint also predicts task type, difficulty, reasoning mode, and expected output length, and supports custom zero-shot labels. For task generation, we construct a task ontology with 23 families, 115 task types, 345 routable subtypes, 1,173 synthetic examples, and an orthogonal axis of 30 domains. Using this structure, we generate 150,000 verifier-scored tasks and 15,000 open-ended tasks. We then train the Qwen3 decoder on these tasks, while explicitly separating learned request prediction from per-task policies for attributes such as eligibility, cost, cache reuse, safety, and sovereignty. Across six LiveBench subsets, the router outperforms the mean candidate; on the selected 1,000-task subset, it achieves an aggregate top-1 score of 0.707 versus 0.696 for the strongest fixed model, with benchmark-dependent gains.
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https://arxiv.org/abs/2609.02292
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Automated Tree Knowledge Graph Construction using Ontology Expansion and Retrieval from Vietnamese History Textbooks
2026-09-01 05:52:50Ket Doan Nguyen, Minh N. H. NguyenAbstract
Hierarchical Knowledge graph (KG)-based retrieval augmented generation (RAG) has emerged as a powerful approach for supporting large language models with structured knowledge. However, there are primary challenges: (i) the lack of methods for automatic KG construction using ontology expansion for low-resource languages such as Vietnamese, (ii) the absence of systematic evaluation for knowledge retrieval strategies leveraging the hierarchical structures. In this paper, we propose an end-to-end pipeline for KG construction and retrieval strategies evaluation. In the KG construction, we employ a three-phase hybrid relation extraction pipeline: intra-batch deduplication via Union-Find, approximate cross-batch search, and LLM extraction with a centroid filter that reduces prompts combined with a five-step dual-LLM validator to prevent bloated ontology. A two-tier architecture consists of unmergeable structural nodes to preserve the document structure and mergeable content nodes. The retrieval evaluation consists of three graph traversal strategies: Top-Down, Horizontal, and Bottom-Up, which are evaluated on a synthetically generated benchmark of 1,210 Vietnamese queries from 109 subgraphs, categorized by five query directions. In this paper, we construct the tree knowledge graph from Vietnamese high school History textbooks (nearly 400 pages) to produce 750 nodes and 4,341 semantic edges with controlled ontology growth from 40 to 41 types. Among experimental graph traversal strategies, the Top-Down strategy with structure surpasses the vector baseline by 4.7 percentage points in NDCG@10. As a result, tree-structural information provides valuable information beyond flat cosine similarity but degrades performance when the query does not require structural context.
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https://arxiv.org/abs/2609.00763
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Bridging Lexical Divergence: LLM-Assisted, Cost-Efficient, Zero-shot Scientific Entity Linking
2026-08-31 18:37:27Md Rasel Khondokar, Qiao Qiao, Farjana Sultana Samia, Nhat Le, Yuepei Li, Qi LiAbstract
Scientific domain entity linking (EL) differs from general domain EL because mentions and entity names often lack lexical overlap. Another challenge is that specialized terminology is used in the scientific domain, which is rarely encountered in models pretrained on general domains. Therefore, models trained on general domains transfer poorly to scientific domains. To address this, in-domain fine-tuning is the natural remedy. However, many scientific domains lack expert-annotated data, motivating the need for a zero-human-annotation approach. Existing zero-shot methods heavily rely on LLMs to generate aliases across entire mention corpora, which incurs substantial computational cost, and those methods provide no mechanism to filter out noise from LLMs. To address these challenges, we propose Sci-ZSEL, a framework that selectively generates entity aliases with an LLM to control computational cost, and applies an ontology-aware filter to remove aliases that semantically drift toward ontology neighbors. Then, filtered aliases are used to construct pseudo-labeled mention-entity pairs for fine-tuning. To enable evaluation of EL under low lexical overlap, we also release a new animal science EL benchmark linked to three livestock trait ontologies, where mentions and entities exhibit substantially lower lexical overlap than in existing benchmarks. Across five benchmarks, Sci-ZSEL outperforms the non-fine-tuned baseline, is most useful on nonoverlapping mentions, and combining it with curated synonyms gives the best performance in most settings.
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URL
https://arxiv.org/abs/2609.00228
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Do General NLP Embeddings Capture Ontological Reasoning?
2026-08-31 18:03:23Hamed Babaei Giglou, Jennifer D'Souza, S\"oren AuerAbstract
General-purpose NLP embedding models perform well on linguistic tasks, but their ability to capture symbolic ontological structure remains unclear. We introduce AVA, a systematic framework for evaluating whether embeddings distinguish logic-sensitive relational semantics in ontologies and knowledge graphs. AVA comprises 171,007 contrastive triplets derived from 163 heterogeneous ontologies using hierarchy inversion, relation substitution, and disjointness injection. Each triplet contains an ontology statement, a semantically equivalent paraphrase, and a logic-sensitive hard negative with contradictory relational meaning. We evaluate more than 25 state-of-the-art embedding models and find substantial limitations: the best model achieves only 0.739 triplet accuracy, while hard negative accuracy falls to 0.135. Fine-tuning improves discrimination by a large margin but transfers poorly to downstream Semantic Web tasks, including taxonomy discovery and ontology alignment. Further analysis suggests that improvements stem partly from perturbation-specific pattern recognition rather than robust ontological understanding. These findings reveal a persistent gap between linguistic representation learning and ontology-level discrimination, challenging the assumption that strong NLP benchmark performance translates to Semantic Web competence.
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https://arxiv.org/abs/2609.00177
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OntoAligner-Ensemble: Voting-Based Fusion across Heterogeneous Ontology Alignment Techniques
2026-08-31 17:44:25Hamed Babaei Giglou, S\"oren Auer, Peio Popov, Mahsa Sanaei, Jennifer D'SouzaAbstract
Ontology alignment (OA) has evolved through several methodological paradigms, ranging from lexical and structural aligners to knowledge graph embedding (KGE) models and, more recently, Large Language Model (LLM)-based approaches. Although modern OA frameworks provide unified ecosystems for deploying these heterogeneous aligners, mechanisms for systematically reconciling their complementary and sometimes conflicting predictions remain relatively underexplored. We present OntoAligner-Ensemble, a modular and aligner-agnostic framework that combines candidate correspondences through a configurable two-stage process comprising voting-based fusion strategies followed by post-fusion selection policies. The framework supports any aligner implemented within OntoAligner that produces candidate correspondences, enabling diverse alignment paradigms to be integrated through a unified decision process. To demonstrate its effectiveness, we instantiate the framework using representative lightweight string-aligner, KGE-based, and Retrieval-Augmented Generation aligners powered by both open-weight and API-based LLMs. We evaluate individual aligners and ensemble configurations across eight benchmark tasks from five OAEI tracks spanning biomedical to beyond-equivalence. The results show that ensemble fusion consistently improves the balance between precision and recall and frequently outperforms standalone aligners across diverse domains. Furthermore, our analysis reveals that ensemble composition directly affects the precision-recall trade-off: heterogeneous cross-paradigm ensembles generally improve precision, whereas homogeneous LLM ensembles more often achieve higher overall F1-scores. These findings demonstrate that systematic ensemble learning offers a robust and reproducible strategy for OA while providing practical guidance for selecting ensemble compositions under different alignment scenarios.
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https://arxiv.org/abs/2608.31137
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When Does Bigger Help? A Controlled Study of LLM Scale for Ontology Learning
2026-08-31 17:30:05Hamed Babaei Giglou, S\"oren Auer, Jennifer D'SouzaAbstract
The effect of Large Language Model (LLM) scale on ontology learning (OL) performance remains insufficiently characterized. We present a controlled evaluation of 13 models spanning dense and Mixture-of-Experts variants from the Qwen3.5 and Qwen3.6 lineages, together with proprietary GPT release variants, using the OntoLearner retrieval-augmented generation pipeline. All models are evaluated with the same embedding model, retrieval configuration, prompt templates, decoding settings, datasets, and metrics on term typing, taxonomy discovery, and non-taxonomic relationship extraction across four biomedical and materials science and engineering ontologies. Within the dense Qwen3.5 lineage, increasing parameter count primarily improves precision rather than recall, with the largest gains occurring between 9B and 27B parameters. However, the effect of scale is neither monotonic nor uniform across tasks and domains. Dense 27B models outperform substantially larger sparse models on term typing, whereas larger Mixture-of-Experts models achieve the strongest open-weight results on taxonomy discovery. Non-taxonomic relationship extraction remains difficult across model scales, particularly for the Materials Data Science ontology. Performance differences across matched Qwen variants and proprietary GPT releases further indicate that architecture and model lineage can outweigh nominal parameter count. These findings show that model size alone is an insufficient selection criterion for OL and provide empirical guidance for reproducible LLM-assisted ontology engineering.
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https://arxiv.org/abs/2608.31118
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Co-Annotator: Expert-Distilled ViT and VLM for Visual and Documentation Guidance in Age-Related Macular Degeneration
2026-08-31 07:09:05Ziheng "Leo" Li, Benjamin Freeman, Akshay Raman, Kavin Aravindhan Rajkumar, Xinxin Fang, Rishabh Srivastava, Steven Feiner, Kaveri A. ThakoorAbstract
Clinical AI often optimizes predictive performance without engaging how clinicians decide where to look and what to write. We present Co-Annotator, which distills expert gaze and dictation into two guidance components: a gaze-aligned Vision Transformer producing fixation-aligned areas of interest (AOIs), and an ontology-bounded vision-language model (VLM) that pre-fills editable biomarker summaries for retinal optical coherence tomography (OCT). We first collect expert gaze and dictations (US1) to train the models, significantly improving diagnostic accuracy and biomarker generation. We then deploy the system with ophthalmology residents: a controlled resident study (US2) confirmed each modality is safe and independently beneficial, with AOI guidance producing lasting perceptual efficiency gains through post-guidance carryover and VLM guidance more than doubling biomarker documentation breadth. In a combined deployment across two academic institutions (US3), providing both modalities simultaneously produced efficiency gains that substantially exceeded either modality alone: correct diagnoses per minute increased by 40% and comment editing time fell by 67%, without compromising diagnostic accuracy. Notably, neither modality improved efficiency during guidance in US2, which makes the in-guidance efficiency gain under combined guidance in US3 the more striking result. Expert-distilled multimodal guidance can remove two distinct clinical workflow bottlenecks at once (visual search overhead and documentation burden) without compromising the diagnostic accuracy clinicians already achieve.
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https://arxiv.org/abs/2608.30352
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